Bioinformatics

The Genomics Facility at Monash University Malaysia is equipped with a total of 14 Linux workstations (some up to 32 CPUs, 128 Gb RAM) to process the large amount of NGS data generated from various projects. In addition, the facility also has access into the High Performance Computing (HPC) Research Infrastructure and is collaborating closely with the team to help staffs in familiarizing the system. Moreover, with affiliations to Monash University Australia, we are also granted access to the Monash Campus Cluster (MCC) which is made up of over 200 servers of different CPU and memory configurations. These resources provide us with the capabilities to handle a variety of projects ranging from small single gene analysis to large genome assemblies.

What we do

We have developed in-house bioinformatics tools that are freely available.

MitoPhAST: an automated tool that (1) identifies annotated protein-coding gene features and generates a standardised, concatenated and partitioned amino acid alignment directly from complete/partial GenBank/EMBL-format mitogenome flat files, (2) generates a maximum likelihood phylogenetic tree using optimised protein models and (3) reports various mitochondrial genes and sequence information in a table format. MitoPhAST is available for download at: https://github.com/mht85/MitoPhAST

 

 

Since the start of the genomics facility in 2013, we have undertaken a variety of projects which require different sets of skills and programs.

Sequence read QC

 Genome assembly and annotation

 

Transcriptomics and RNA-seq analysis

 

Mitogenome assembly and annotation

 

Metagenomics

 

Microsatellite detection and primer design

 

Phylogenetic analysis

 

Giving back to Monash

In addition to providing bioinformatics services, we truly believe in empowering the students and staff of Monash University Malaysia with the skills and knowledge required to conduct various NGS analysis for their own projects. To do so, an additional Linux workstation (16 CPUs, 64 Gb RAM) with a licensed CLC Genomics Workbench software has been set up for shared use (please contact Dr. Gan Han Ming for more information on getting access to the workstation). We have also successfully conducted several NGS workshops with more to come. In the mean time, we welcome students and staff alike to drop by the office with any questions and queries regarding NGS, its applications and analysis.